In September 1857, the Baker-Fancher party, an emigrant group from Arkansas, camped at Mountain Meadows, a staging area in southern Utah used to prepare for the long crossing of the Mojave Desert by groups travelling westward to California.[5] They were attacked by a combined group of Native Americans and Mormon militiamen dressed as Native Americans. On the third day of the siege, Lee (not dressed as a Native American) approached the Baker-Fancher encirclement under cover of a white flag and convinced the emigrants to surrender their weapons and property to the Mormons in return for safe conduct to nearby Cedar City. The emigrants accepted the offer and surrendered, however approximately 120 of the Baker-Fancher party were then killed by Mormon militia and Paiute Indians, leaving only about 17 small children as survivors.[6][7] William Ashworth notes in his autobiography that after the massacre, the "leaders among the white men had bound themselves under the most binding oaths to never reveal their part in it." Lee told Brigham Young that the Indians had been solely responsible, that "no white men were mixed up in it."[8] Lee later maintained that he had acted under orders from his militia leaders, under protest, and remained active in Mormonism and local government for several years afterwards.

In 1874, Lee was arrested and tried for leading the massacre. The first trial ended inconclusively with a hung jury, seemingly because of the prosecution's attempt to portray Brigham Young as the true mastermind of the massacre. A second trial in 1877, in which the prosecution placed the blame squarely on Lee's shoulders, ended with his conviction and he was sentenced to death.[9] Lee never denied his own complicity, but claimed he had not personally killed anyone. He said he had been a vocally reluctant participant and later a scapegoat meant to draw attention away from other Mormon leaders who were also involved. Lee further maintained that Brigham Young had no knowledge of the event until after it happened. However, in the Life and Confessions of John D. Lee he (or an editor) wrote, "I have always believed, since that day, that General George A. Smith was then visiting southern Utah to prepare the people for the work of exterminating Captain Fancher's train of emigrants, and I now believe that he was sent for that purpose by the direct command of Brigham Young."[10]

Drawing of Lee's execution.

On March 23, 1877, Lee was executed by firing squad at Mountain Meadows on the site of the 1857 massacre. His last words included a reference to Young: "I do not believe everything that is now being taught and practiced by Brigham Young. I do not care who hears it. It is my last word... I have been sacrificed in a cowardly, dastardly manner."[11] On April 20, 1961, the LDS Church posthumously reinstated Lee's membership in the church.[12]

^Haymond, Jay M. (1994), "Lee, John D.", in Powell, Allan Kent, Utah History Encyclopedia, Salt Lake City, Utah: University of Utah Press, ISBN0874804256, OCLC30473917, In January 1856 Lee was appointed U.S. government Indian Agent in the Iron County environs. His job was to distribute tools, seed, and supplies, and to assist the Indians with farming methods.